The Belgian striker, who is currently on loan with the French club after agreeing to join Liverpool in the summer, struck minutes into the second period to send Lille into the lead.
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The youngster then set up on-loan Manchester City youngster Marcos Lopes, who finished from close range to send the home side into a two-goal lead with 50 minutes on the clock.
Clear chances were at a premium throughout the contest, with the majority of efforts from both teams failing to test the opposing goalkeeper.
Nantes did threaten in the latter stages, but Lille held on to keep their clean sheet intact.
The result has moved Lille to the top of the Ligue 1 table, while Nantes remain in 10th position.
Next up for the home side is a Europa League clash with Krasnodar on Thursday, while Nantes return to league action at home to Nice next Saturday.